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Enzyme Diversity of Nitrifying Organisms and Their Biotechnological Application

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Enzyme Diversity of Nitrifying Organisms and Their Biotechnological Application Enzyme Diversity of Nitrifying Organisms and Their Biotechnological Application Diplomarbeit zur Erlangung des akademischen Grades Master of Science in Engineering der Fachhochschule Campus Wien Master-Studiengang Bioverfahrenstechnik Vorgelegt von: Mag. Dr. Andrea Kahlbacher, BSc Personenkennzeichen: c1810540006 FH-Hauptbetreuerin: Univ.-Prof. Dipl.-Ing. Dr. Kristina Djinovic-Carugo Zweitprüfer: Mag. Dr. Andreas Franz Abgabetermin: 23.08.2020 FH Campus Wien University of Applied Sciences/Fachbereich Bioengineering FH Campus Wien University of Applied Sciences/Fachbereich Bioengineering Erklärung: Ich erkläre, dass die vorliegende Diplomarbeit von mir selbst verfasst wurde und ich keine anderen als die angeführten Behelfe verwendet bzw. mich auch sonst keiner unerlaubten Hilfe bedient habe. Ich versichere, dass ich diese Diplomarbeit bisher weder im In- noch im Ausland (einer Beurteilerin/einem Beurteiler zur Begutachtung) in irgendeiner Form als Prüfungsarbeit vorgelegt habe. Weiters versichere ich, dass die von mir eingereichten Exemplare (ausgedruckt und elektronisch) identisch sind. Datum: ………………………… Unterschrift: ………………………………………………… Abstract Die vorliegende Arbeit befasst sich mit der Diversität von Enzymen nitrifizierender Organismen sowie den damit verbundenen biotechnologischen Anwendungsmöglichkeiten und besteht aus zwei einander ergänzenden Teilen. Nitrifikation ist ein bedeutender Teil des Stickstoffzyklus und beschreibt die Oxidation von Ammonium zu Nitrit und anschließend zu Nitrat. Dabei wird Ammonium von Ammonium- oxidierenden Bakterien (AOB) oder Ammonium-oxidierenden Archaea (AOA) umgewandelt, während Nitrit-oxidierende Bakterien (NOB) Nitrit zu Nitrat verstoffwechseln. Beide Gruppen können jeweils nur ein Substrat (Ammonium oder Nitrit) oxidieren. Die funktionale Teilung der Nitrifikation in diese zwei Teilschritte galt lange als opinio communis, bis diese 2015 durch die Entdeckung von Comammox-Bakterien geändert werden musste. Comammox ist ein Akronym und steht für complete ammonia oxidizer; diese Bakterien können daher sowohl Ammonium zu Nitrit als auch Nitrit zu Nitrat oxidieren. Teil I der Arbeit beschäftigt sich mit zwei Proteinen (Nxr und MCO) eines Comammox Bakteriums (Candidatus Nitrospira inopinata) und einer Cyanase eines Ammonium- oxidierenden Archaeon (Nitrososphaera gargensis). Der Proteinkomplex Nitritoxidoreduktase (Nxr) besteht aus drei Untereinheiten und ist das Schlüsselenzym für die Oxidation von Nitrit zu Nitrat. Anders als bei anderen Nitrifizierern weist Nxr von Nitrospira Arten eine periplasmische statt einer zytoplasmischen Orientierung auf, wodurch eine Ansammlung toxischen Nitrits im Zytoplasma verhindert werden kann. Die Multicopperoxidase (MCO) von Ca. N. inopinata ist ein neuartiges Protein, dessen Funktion noch unbekannt ist. Ziel ist es, für beide Proteine einen Weg zu finden sie zu klonieren, zu exprimieren und anschließend aufzureinigen. Die Cyanase stammt von N. gargensis und katalysiert die Reaktion von Cyanat zu Carbamat, das anschließend zu Ammoniak und Kohlendioxid zerfällt. Im Vorfeld konnte gezeigt werden, dass die N. gargensis der erste bekannte Organismus ist, der Cyanat als einzige Energiequelle nutzen kann. Das Enzym konnte erfolgreich exprimiert und aufgereinigt werden. Das aufgereinigte Protein ist der Ausgangspunkt für weitere biophysikalische Analysen; mithilfe von Size Exclusion Multiangle Light Scattering (SEC-MALS) konnte festgestellt werden, dass das Enzym Cyanase als Oktamer vorliegt. Kinetische Analysen haben gezeigt, dass die Affinität der Cyanase von N. gargensis auf das Substrat Cyanat höher ist als bei anderen Organismen (z.B. E. coli). Teil II befasst sich mit dem möglichen Einsatz von Comammox Bakterien in modernen Abwasseranlagen. Dazu wird zuerst ein Überblick über die Hauptkläranlage Wien gegeben. Anschließend folgt eine Zusammenfassung von neuen Technologien basierend auf Anammox- Bakterien (anaerobic ammonia oxidation). Dabei wird die anaerobe Oxidation von Ammonium zu Nitrit mit der Reduktion von Nitrit zu Stickstoff (N2) gekoppelt. In der Abwassertechnologie wird der Anammox-Prozess mit der aeroben Oxidation von Ammonium zu Nitrit kombiniert. Zum Schluss wird ein Ausblick über mögliche Anwendungen von Comammox in der Hauptkläranlage Wien gegeben. Abstract The present thesis deals with the diversity of enzymes of nitrifying organisms and the associated biotechnological applications. It consists of two complementary parts. Nitrification is an important part of the nitrogen cycle and describes the oxidation of ammonia to nitrite and subsequentially to nitrate. During this process, ammonia is converted by ammonia-oxidizing bacteria (AOB) or ammonia-oxidizing archaea (AOA), while nitrite- oxidizing bacteria (NOB) metabolize nitrite to nitrate. Both groups can only oxidize one substrate (ammonia or nitrite). The functional division of nitrification into these two sub-steps was long considered opinio communis, until this had to be changed in 2015 with the discovery of Comammox bacteria. Comammox is an acronym and stands for complete ammonia oxidizer; these bacteria can therefore oxidize ammonia via nitrite to nitrate. Part I of the work deals with two proteins (Nxr and MCO) of a Comammox bacterium (Candidatus Nitrospira inopinata), as well as with a cyanase of an ammonium oxidizing archaeon (Nitrososphaera gargensis). The protein complex nitrite oxidoreductase (Nxr) consists of three subunits and is the key enzyme for the oxidation of nitrite to nitrate. Unlike other nitrifiers, Nxr of Nitrospira exhibits periplasmic rather than cytoplasmic orientation, which can prevent accumulation of toxic nitrite in the cytoplasm. The multicopperoxidase (MCO) of Ca. N. inopinata is a novel protein whose function is still unknown. The goal is to find a way to clone, express and purify both proteins. The cyanase comes from N. gargensis and catalyzes the reaction of cyanate to carbamate, which then decomposes to ammonia and carbon dioxide. It could be shown beforehand that N. gargensis is the first known organism that can use cyanate as its only energy source. The enzyme was successfully expressed and purified. The purified protein is the starting point for further biophysical analyses; with the help of size exclusion multiangle light scattering (SEC- MALS) it could be determined that the enzyme cyanase is present as an octamer. Kinetic analyses have shown that the affinity of the cyanase of N. gargensis to substrate cyanate is higher than in other organisms (e.g. E. coli). Part II deals with the possible use of Comammox bacteria in modern wastewater plants. For this purpose, an overview of Vienna’s main wastewater treatment plant is given first. This is followed by a summary of new technologies based on Anammox (anaerobic ammonia oxidation) bacteria. The anaerobic oxidation of ammonia to nitrite is coupled with the reduction of nitrite to nitrogen (N2). In wastewater technology the anammox process is combined with the aerobic oxidation of ammonia to nitrite. Finally, an outlook on possible applications of Comammox in Vienna’s main wastewater treatment plant is given. Acknowledgments First and foremost, I would like to express my gratitude to my supervisor Univ.-Prof. Dr. Dipl. Ing. Kristina Djinovic-Carugo, who has given me the opportunity to do this master project in her lab. With her valuable feedback she has contributed substantially to this thesis. Dr. Andreas Franz has sparked my interest in wastewater treatment and opened my eyes to this fascinating world. I would like to thank him not only for this, but also for his assistance during the writing. I want to express my deepest gratitude to Mag. Dr. Georg Mlynek, who has been my mentor and has always had an open ear for all my problems. Thanks is also due to Mag. Julius Kostan, PhD and Antonio Sponga, MSc for their help in the lab. Dr. Chris Sedlacek from the department for microbial ecology has helped me a lot with the cyanase, and I would like to thank him for that. Lastly, I would like to thank all my colleagues from the Djinovic Lab for all their support, help and shared moments, which I will always cherish. Table of contents PART I 1 Introduction ..................................................................................................................................... 3 1.1 Nitrification .............................................................................................................................. 3 1.2 Candidatus Nitrospira inopinata ............................................................................................. 4 1.2.1 Nitrite oxidoreductase (Nxr) of Ca. N. inopinata ............................................................. 5 1.2.2 Multicopperoxidase (MCO) from Ca. N. inopinata .......................................................... 7 1.3 Nitrososphaera gargensis ........................................................................................................ 7 1.3.1 Cyanase from N. gargensis .............................................................................................. 8 1.4 Research questions................................................................................................................ 10 2 Materials and methods ................................................................................................................. 12 2.1 Cloning ................................................................................................................................... 12 2.2 Small-scale expression ..........................................................................................................
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